I have not found papers that satisfy me as a response to your question, but I will exhibit two examples focusing on the mass of Standard Model fermions, which comes from yukawa couplings to the Higgs field. To predict the masses would mean to predict the yukawa coefficients, and the vacuum expectation value of the Higgs field.
This 2002 paper describes "intersecting braneworlds". The fermions are strings at the intersection of branes, the Higgs is a string between two parallel branes, the yukawa interaction involves contact between those strings, and the strength of the interaction depends on the area of the surface they trace out in order to come into contact, see figure 1 and equation 3.1. The paper specifies a particular brane geometry that gives the gauge fields and particle generations of the standard model, and then asks if the exact spacing and angles of the branes can be chosen so as to give the observed values of the SM parameters. The authors say yes, see various tables in part 4.
But that still leaves open the question whether any of those exact brane configurations are stable. Or would the branes move away from those positions, spoiling the quantitative match? Here see the second paragraph on page 26: the authors hope that one of these configurations might be produced as a stable perturbation of a dynamically favored symmetrical configuration.
I believe this paper turned out to be flawed (see the disclaimer added to the abstract), but I chose it because it's easy to point out where and how they try to match reality.
The other paper comes from 2013 and I chose it because I think it's considered an important paper within a major school of thought, that it's still the state-of-the-art way within "F-theory" to give the top quark its large mass. Here they speak of yukawa couplings arising from "wavefunction overlap" but otherwise it's similar, the fermions and the Higgs are localized near each other in the extra dimensions... The calculations occur in part 6 and again, the algebra is followed by an attempt (6.14) to identify plausible specific values for properties of the compactification that will give an empirically correct outcome (6.15).
I'll also mention
Kaplunovsky & Louis 1995 as an example of a theory paper that's not about a particular model, but rather, about the general form of the relationship between couplings in a field theory, and parameters coming from a deeper theory like string theory.